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Re: Why is my program so slow even though I've used hashes?

by akho (Hermit)
on May 28, 2009 at 18:05 UTC ( #766716=note: print w/replies, xml ) Need Help??

in reply to Why is my program so slow even though I've used hashes?

What could
$domchain =~/\S/g; $pdbchain =~/\S/g; chomp($domchain); chomp($pdbchain);
possibly accomplish?

I tried to fix some things in the code below, but, naturally, I could't try to run it (as I don't have the files).

use strict; use warnings FATAL => 'all'; use autodie; my $dir = "<my directory>"; my ( $dom_file_name, $csa_file_name ) = @ARGV; my %csa_hash; my %dom_hash; open my $csa_file, '<', $csa_file_name; while ( my $csa = <$csa_file> ) { my @csa_data = split( /\,/, $csa ); $csa_hash{ $csa_data[0] . $csa_data[3] } = $csa_data[4]; } close($csa_file); open my $dom_file, '<', $dom_file_name; while ( my $dom = <$dom_file> ) { my @dom_data = split /\s+/, $dom; my $domain = $dom_data[0]; next if exists $dom_hash{$domain}; open my $ind_dom_file, '<', $dir . $domain; while ( my $line = <$ind_dom_file> ) { chomp $line; my @ff = split /\s+/, $line; my $number = $ff[5]; my $CA = $ff[2]; push @{ $dom_hash{$domain} }, $number if $CA eq 'CA'; } close $ind_dom_file; } close $dom_file; while ( my ( $protein_dom, $residues_ref ) = each %dom_hash ) { for my $residue ( @{$residues_ref} ) { my $dom_chain = substr( $protein_dom, 0, 5 ); if ( $residue eq $csa_hash{$dom_chain} ) { print "$dom_chain $residue\n"; } } }

The idea was that it does the same thing as your code, but faster.

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